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PROTECT Pathogen Browser

protect_genomedepot

Domain

Philosophy

Support pathogen surveillance research. Catalog pathogen genomes, track strain variation, and enable comparative genomic analysis for public health applications.

Data sources: PROTECT

Scale

6
tables

Schema Browser

Tables (2)

browser_genome browser_gene_sampled

browser_genome

Column Type Description
id string **Primary Key**
name string Genome name
description string Description
contigs string Number of contigs
size string Genome size
genes string Number of genes
json_url string JSON metadata URL
pub_date string Publication date
external_url string External link
external_id string External identifier
gbk_filepath string GenBank file path
sample_id string FK -> `browser_sample`
strain_id string FK -> `browser_strain`
taxon_id string FK -> `browser_taxon`

Sample Queries

Get pathogen genomes

SELECT *
FROM protect_genomedepot.browser_genome
LIMIT 20

Projects Using This Collection

CF Protective Microbiome Formulation Design

Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competiti...

Start Exploring

Access the full PROTECT Pathogen Browser data through BERDL JupyterHub.

Open JupyterHub